├── .coveragerc_parallel ├── .coveragerc_serial ├── .gitattributes ├── .github ├── my_actions │ ├── branch_dispatch │ │ ├── action.yml │ │ ├── dist │ │ │ └── index.js │ │ ├── index.js │ │ ├── package-lock.json │ │ └── package.json │ ├── check_existence │ │ ├── action.yml │ │ ├── dist │ │ │ └── index.js │ │ ├── index.js │ │ ├── package-lock.json │ │ └── package.json │ ├── check_membership │ │ ├── action.yml │ │ ├── dist │ │ │ └── index.js │ │ ├── index.js │ │ ├── package-lock.json │ │ └── package.json │ └── reply_sender │ │ ├── action.yml │ │ ├── dist │ │ └── index.js │ │ ├── index.js │ │ ├── package-lock.json │ │ └── package.json ├── update_sophios_config.py └── workflows │ ├── branch_dispatch.md │ ├── branch_dispatch_pull_request.yml │ ├── branch_dispatch_push.yml │ ├── branch_dispatch_repository_dispatch.yml │ ├── build_wheel.yml │ ├── docker_build.yml │ ├── docker_build_plugins.yml │ ├── fuzzy_compile_weekly.yml │ ├── lint_and_test.yml │ ├── lint_and_test_macos.yml │ ├── publish_rest_docker.yml │ ├── run_workflows.yml │ ├── run_workflows_weekly.yml │ ├── test_and_publish_pypi.yml │ └── token.md ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── .vscode ├── extensions.json ├── launch.json └── settings.json ├── LICENSE ├── MANIFEST.in ├── README.md ├── codespellwords.txt ├── conftest.py ├── cwl_adapters ├── ambiguous.cwl ├── append.cwl ├── array_float.cwl ├── array_indices.cwl ├── array_int.cwl ├── cat.cwl ├── check_linear_fit.cwl ├── dup.cwl ├── echo.cwl ├── echo_3.cwl ├── fail.cwl ├── file_watchers │ └── cwl_subinterpreter.cwl ├── filter_array.cwl ├── glob_pattern.cwl ├── identity.cwl ├── nvidia_smi.cwl ├── random_subset_rows.cwl ├── scatter_plot.cwl ├── subdirectory.cwl ├── toString.cwl ├── touch.cwl └── wget_xlsx.cwl ├── docker ├── Dockerfile_amazon ├── Dockerfile_debian ├── Dockerfile_fedora ├── Dockerfile_redhat ├── Dockerfile_ubuntu ├── Dockerfile_ubuntu_REST ├── docker-compose.yml └── dockerBuild.sh ├── docs ├── Makefile ├── _static │ └── style.css ├── _templates │ └── layout.html ├── advanced.md ├── code_completion.png ├── conf.py ├── dev │ ├── algorithms.md │ ├── api.rst │ ├── codingstandards.md │ ├── devguide.md │ ├── gitetiquette.md │ └── installguide.md ├── index.rst ├── installguide.md ├── make.bat ├── overview.md ├── requirements.txt ├── tutorials │ ├── append_twice.wic │ ├── conditional_example.wic │ ├── config_ci.json │ ├── echo_multi_scatter.wic │ ├── fail.wic │ ├── helloworld.md │ ├── helloworld.wic │ ├── multistep.md │ ├── multistep1.wic │ ├── multistep1.wic.gv.png │ ├── multistep2.wic │ ├── multistep2.wic.gv.png │ ├── multistep3.wic │ ├── multistep3.wic.gv.png │ ├── naming_conventions.md │ ├── naming_conventions.wic │ ├── naming_conventions.wic_no_flag.png │ ├── naming_conventions.wic_with_flag.png │ ├── naming_conventions_explicit.wic │ ├── naming_conventions_explicit.wic.gv.png │ ├── subworkflows.md │ ├── test_rand_fail.wic │ └── tutorials.rst ├── userguide.md └── validation.md ├── examples ├── scattering_scaling.wic ├── scripts │ ├── Dockerfile_check_linear_fit │ ├── Dockerfile_random_subset_rows │ ├── Dockerfile_scatter_plot │ ├── check_linear_fit.py │ ├── ground_truth_multistep1.json │ ├── helloworld_pyapi.py │ ├── multistep1_pyapi.py │ ├── multistep1_toJson_pyapi.py │ ├── python_cwl_driver.py │ ├── random_subset_rows.py │ ├── scatter_plot.py │ ├── scatter_pyapi.py │ ├── when_pyapi.py │ └── workflow_types.py ├── secrets_echo.wic └── test_nvidia_smi.wic ├── install ├── install_biobb_adapters.sh ├── install_conda.bat ├── install_conda.sh ├── install_image-workflows.sh ├── install_mm-workflows.sh ├── install_pypy.sh ├── install_system_deps.bat ├── install_system_deps.sh ├── install_timeseriesplots.sh ├── system_deps.yml └── system_deps_windows.yml ├── ipycytoscape.ipynb ├── pyproject.toml ├── setup.py ├── src └── sophios │ ├── __init__.py │ ├── _version.py │ ├── apis │ ├── __init__.py │ ├── python │ │ ├── __init__.py │ │ ├── _types.py │ │ ├── api.py │ │ └── api_config.py │ ├── rest │ │ ├── __init__.py │ │ └── api.py │ └── utils │ │ ├── __init__.py │ │ ├── converter.py │ │ ├── ict │ │ ├── __init__.py │ │ └── ict_spec │ │ │ ├── __init__.py │ │ │ ├── cast.py │ │ │ ├── hardware │ │ │ ├── __init__.py │ │ │ └── objects.py │ │ │ ├── io │ │ │ ├── __init__.py │ │ │ └── objects.py │ │ │ ├── metadata │ │ │ ├── __init__.py │ │ │ └── objects.py │ │ │ ├── model.py │ │ │ ├── tools │ │ │ ├── __init__.py │ │ │ └── cwl_ict.py │ │ │ └── ui │ │ │ ├── __init__.py │ │ │ └── objects.py │ │ ├── input_object_schema.json │ │ └── wfb_util.py │ ├── ast.py │ ├── cli.py │ ├── compiler.py │ ├── config_basic.json │ ├── cwl_subinterpreter.py │ ├── inference.py │ ├── inlineing.py │ ├── input_output.py │ ├── main.py │ ├── plugins.py │ ├── post_compile.py │ ├── py.typed │ ├── python_cwl_adapter.py │ ├── run_local.py │ ├── run_local_async.py │ ├── schemas │ ├── __init__.py │ └── wic_schema.py │ ├── utils.py │ ├── utils_cwl.py │ ├── utils_graphs.py │ ├── utils_yaml.py │ └── wic_types.py ├── tests ├── __init__.py ├── data │ ├── __init__.py │ ├── cwl │ │ └── helloworld.cwl │ ├── ict_data │ │ ├── czi_extract │ │ │ ├── czi_extract_clt.json │ │ │ └── czi_extract_ict.json │ │ ├── label_to_vector │ │ │ ├── label_to_vector_clt.json │ │ │ └── label_to_vector_ict.json │ │ └── ome_conversion │ │ │ ├── ome_conversion_clt.json │ │ │ └── ome_conversion_ict.json │ └── wfb_data │ │ └── multi_node │ │ ├── multi_node_wfb.json │ │ └── multi_node_wfb_truth.json ├── rest_wfb_objects │ ├── bbbc_download_wfb.json │ ├── multi_node.json │ ├── multi_node_inline_cwl.json │ ├── multi_node_wfb.json │ ├── single_node.json │ └── single_node_bbbc_download.json ├── test_cli_flags.py ├── test_compile_python_workflows.py ├── test_examples.py ├── test_fix_payload.py ├── test_fuzzy_compile.py ├── test_ict_to_clt_conversion.py ├── test_rest_core.py ├── test_rest_wfb.py ├── test_scattering_scaling.py └── test_setup.py ├── timeseriesplots_labels.json ├── versioneer.py └── wicStyle.json 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